haven't made one of these,but wondering if you did it in rows or basically worked on quarter of the quilt at a time? I've always seen it worked on in quarters, I'm guessing to keep it straighter. the loose weave of the shot cotton may be a problem too. Try to really cover the wavy areas with spray starch and when almost dry, hit with steam--that is trick that long arm quilters use to deal with wavy borders. also, don't know how you plan to quilt it, but using a double bat (80/20 on bottom and wool or med loft poly on top) will also "fill in" some of the puckers. Good luck--very pretty.
(P.S. I'd probably not make larger with that much waving unless I took apart enough to solve the issue first)